I would like to add a pane to the gravity skin.
top content to the Contact us page and/or make the home page to have 3 col in the center.

I am fairly new with DNN - watched teh video in the Resources but I am still a bit unclear.

I host with Powerdnn and I use Filezilla for FTP.

Where should these changes be made from the FTP - the site or Powerdnn??
When making changes what is the process for the FTP - it asks If I want to delete local file-- should I?

If you were able to add a pane then that means you found the skin folder and modified an .ascx file. In that same folder there is a skin.css file that works together with the .ascx file to apply CSS to your DIVS, Panes, etc.  Your pane name most likely had an ID and a Class attribute in it. Go to your .CSS file and look at the styles specified for the ID and/or Class. If they do not fit your needs simply give your pane a new class name and add it to your skin.css file and you'll be able to style it as you wish. 

The skinning section of the video library is your best friend in this case.